Bromine in the structure of Flock House Virus B2-Dsrna Complex (P212121) (pdb 2az0)

The binding sites of Bromine atom in the structure of Flock House Virus B2-Dsrna Complex (P212121) (pdb code 2az0). This binding sites where shown with 5.0 Angstroms radius around Bromine atom. The 2az0 structure was solved by J.A.CHAO, J.H.LEE, B.R.CHAPADOS, E.W.DEBLER, A.SCHNEEMANN, J.R.WILLIAMSON, with X-Ray Crystallography technique, brief refinement statistics is given in the table below:

Resolution (A)

34.4-2.6

Space group

P212121

a (A)

50.261

b (A)

86.232

c (A)

94.338

alpha (°)

90.00

beta (°)

90.00

gamma (°)

90.00

Rfactor (%)

24.1

Rfree (%)

26.9

Bromine Binding Sites:

Bromine binding site 1 out of 6 in 2az0

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 1 of Bromine in the PDB 2az0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: C: A3, C: 5bu4, C: Hoh19,

conact list:

Atom

Atom

Distance (A)

Br

N9 C:A3

3.92

Br

C3' C:A3

4.35

Br

C8 C:A3

3.43

Br

C6 C:A3

4.46

Br

C5 C:A3

3.74

Br

N6 C:A3

4.83

Br

C1' C:A3

4.76

Br

N7 C:A3

3.33

Br

C4 C:A3

4.11

Br

C2' C:A3

4.46

Br

N3 C:5bu4

4.14

Br

C2 C:5bu4

4.71

Br

C6 C:5bu4

2.82

Br

N1 C:5bu4

4.13

Br

C5 C:5bu4

1.89

Br

P C:5bu4

4.69

Br

C4 C:5bu4

2.89

Br

OP2 C:5bu4

3.79

Br

BR C:5bu4

0.00

Br

O5' C:5bu4

4.46

Br

O4 C:5bu4

3.18

Br

O C:Hoh19

4.99

interactive model:

Bromine binding site 2 out of 6 in 2az0

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 2 of Bromine in the PDB 2az0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: C: G11, C: 5bu12, C: C13,

conact list:

Atom

Atom

Distance (A)

Br

N9 C:G11

3.86

Br

N3 C:G11

4.53

Br

C3' C:G11

4.24

Br

C8 C:G11

3.75

Br

C2 C:G11

4.96

Br

C6 C:G11

4.39

Br

N1 C:G11

4.91

Br

C5 C:G11

3.76

Br

C1' C:G11

4.59

Br

N7 C:G11

3.72

Br

O3' C:G11

4.92

Br

C4 C:G11

3.87

Br

C2' C:G11

4.15

Br

O6 C:G11

4.95

Br

N3 C:5bu12

4.11

Br

C2 C:5bu12

4.68

Br

C6 C:5bu12

2.80

Br

N1 C:5bu12

4.11

Br

C5 C:5bu12

1.87

Br

P C:5bu12

4.50

Br

C4 C:5bu12

2.86

Br

OP2 C:5bu12

3.57

Br

BR C:5bu12

0.00

Br

O5' C:5bu12

4.30

Br

O4 C:5bu12

3.13

Br

C5 C:C13

4.57

Br

C4 C:C13

5.00

Br

N4 C:C13

4.61

interactive model:

Bromine binding site 3 out of 6 in 2az0

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 3 of Bromine in the PDB 2az0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: C: A15, C: 5bu16,

conact list:

Atom

Atom

Distance (A)

Br

N9 C:A15

3.90

Br

C3' C:A15

4.30

Br

C8 C:A15

3.43

Br

C6 C:A15

4.57

Br

C5 C:A15

3.81

Br

C1' C:A15

4.72

Br

N7 C:A15

3.39

Br

C4 C:A15

4.11

Br

C2' C:A15

4.39

Br

O5' C:A15

4.83

Br

N3 C:5bu16

4.14

Br

C2 C:5bu16

4.70

Br

C6 C:5bu16

2.80

Br

N1 C:5bu16

4.11

Br

C5 C:5bu16

1.89

Br

P C:5bu16

4.71

Br

C4 C:5bu16

2.91

Br

OP2 C:5bu16

3.78

Br

BR C:5bu16

0.00

Br

O5' C:5bu16

4.49

Br

O4 C:5bu16

3.20

interactive model:

Bromine binding site 4 out of 6 in 2az0

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 4 of Bromine in the PDB 2az0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: D: A3, D: 5bu4,

conact list:

Atom

Atom

Distance (A)

Br

N9 D:A3

3.86

Br

N3 D:A3

4.89

Br

C3' D:A3

4.18

Br

C8 D:A3

3.47

Br

C6 D:A3

4.45

Br

C5 D:A3

3.74

Br

N6 D:A3

4.89

Br

C1' D:A3

4.66

Br

N7 D:A3

3.40

Br

O3' D:A3

4.84

Br

C4 D:A3

4.03

Br

C2' D:A3

4.22

Br

N3 D:5bu4

4.12

Br

C2 D:5bu4

4.68

Br

C6 D:5bu4

2.79

Br

N1 D:5bu4

4.10

Br

C5 D:5bu4

1.87

Br

P D:5bu4

4.42

Br

C4 D:5bu4

2.87

Br

OP2 D:5bu4

3.52

Br

BR D:5bu4

0.00

Br

O5' D:5bu4

4.19

Br

O4 D:5bu4

3.16

interactive model:

Bromine binding site 5 out of 6 in 2az0

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 5 of Bromine in the PDB 2az0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: D: G11, D: 5bu12,

conact list:

Atom

Atom

Distance (A)

Br

N9 D:G11

3.66

Br

N3 D:G11

4.50

Br

C3' D:G11

3.98

Br

C8 D:G11

3.48

Br

C2 D:G11

4.98

Br

C6 D:G11

4.31

Br

N1 D:G11

4.90

Br

C5 D:G11

3.60

Br

C1' D:G11

4.39

Br

N7 D:G11

3.46

Br

O3' D:G11

4.69

Br

C4 D:G11

3.75

Br

C2' D:G11

3.95

Br

O5' D:G11

5.00

Br

O6 D:G11

4.86

Br

N3 D:5bu12

4.12

Br

C2 D:5bu12

4.68

Br

C6 D:5bu12

2.79

Br

N1 D:5bu12

4.10

Br

C5 D:5bu12

1.87

Br

P D:5bu12

4.33

Br

C4 D:5bu12

2.87

Br

OP2 D:5bu12

3.44

Br

BR D:5bu12

0.00

Br

O5' D:5bu12

4.19

Br

O4 D:5bu12

3.17

interactive model:

Bromine binding site 6 out of 6 in 2az0

Click to enlarge

Click to enlarge

Mono- and Stereo- picture of 5.0 Angstrom coordination sphere 6 of Bromine in the PDB 2az0. Coordination sphere was calculated for all residues within 5.0 Angstroms distance from the central Bromine atom, shown by VdW sphereResidues shown as a stick model or VDW spheres: D: A15, D: 5bu16,